What you say isn't really true, not universally. There are lots and lots of stories where dragons are just animals at best, or evil monsters.
But we get what you mean.
Largely, it's because dragons have been part of human mythology since before civilization. There are pre-civilization artifacts that are carved into the shapes of dragons. Dragons are the prototypical/primordial deities. They're the predator as force of nature, and always have been. And if you want to learn the secrets of nature, you either go talk to a dragon, or you kill one and drink its blood or eat its heart. We're all steeped in those stories, and so we learn to treat them that way and write more stories like them.
On top of that, dragons were the enemy of the Christian god for a long, long time. There are lots of stories about knights and saints riding out and defeating dragons as part of the church's efforts to colonize Europe and the rest of the world. That catches the modern imagination by casting dragons in the light of being victims of and the resistance to the church's oppression. And so a lot of authors who've experienced harm at the hand of some form of Christianity or another will lift dragons up as something more pure and almost heroic, but in a chaotic and natural kind of way. As representatives of the Earth itself.
*waves*
Hi!
Read girldragongizzard for more! :D
(There's also a bit of orientalism going on, because Chinese Lung, which everyone generally calls dragons, have been the celestial rulers for thousands of years, and those of us who like dragons in general to be powerful tend to fall in love with the idea of the Lung and adopt many of their traits for our own dragons.)
